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2023-03-28Slurm & LSF: How to Checkpoint & Terminate (#3778)Gravatar Axel Huebl 1-0/+22
* Slurm: How to Checkpoint & Terminate Add a first concrete example how to gracefully checkpoint and terminate a WarpX simulation that runs into an HPC system's walltime. If this works well, we will add this to all HPC templates. * Signal Handling for LSF x-ref https://www.ibm.com/docs/en/spectrum-lsf/10.1.0?topic=options-wa * Simplified
2023-03-28Output enabled diagnostics (and checkpoint) on interrupt (#3790)Gravatar Roelof Groenewald 1-2/+5
* output enabled diagnostics on interupt by default * add flag to output LastTimestep diagnostics if the PIC loop was interrupted by an OS signal
2023-03-28Fix: openPMD Weighting Loading (#3783)Gravatar Ilian Kara-Mostefa 2-20/+14
* Fix: openPMD Weighting Loading This fixes the loading of openPMD beams with per-particle weighting. The previous implementation forgot to `flush()` the data of the weighting attribute and assumed the weighting of the first particle applies to all particles of the loaded beam. This change loads the weighting for each particle. * Updating the documentation: removed re-scaling feature while using the "external file" injection style. * Issue a warning if a nonzero q_tot is found in the inputs file * Formatting and comments Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2023-03-28Fix restart btd (#3734)Gravatar Revathi Jambunathan 13-40/+344
* Correct calculation of m_t_lab * write BTD related restart, read, and init data before and after accordingly * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * write snapshot domain lo and hi in moving window dir * write lo and hi of snapshot domain for all dimensions * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * clean up * more meta data and redefine snapshot geom, buffer mf and write to new dir for plotfile instead of merging * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * use virtual functions * empty else condition * remove commented line * fix error in returning k-index. Thanks CI * doxygen comments * doxygen comments * more doxygen --------- Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>
2023-03-28Fix bugs related to azimuthal modes for multi-J algo in RZ geometry (#3764)Gravatar Olga Shapoval 3-38/+62
* Bug fix: loop over all azimuthal modes taking into account the shift `mode*n_fields` * Bug fix: added missing speed of light factor in coefficient `c2` * Bug fix: added missing `mode` as fourth optional component in `X5(i,j,k,mode)` and `X6(i,j,k,mode)` coefficients, used only with RZ multi-J averaged PSATD * Reset benchmark of `multi_J_rz_psatd`
2023-03-27Update Paper Badge to GBGravatar Axel Huebl 1-1/+1
Follow-up to #3718
2023-03-27Enable calling SortParticlesForDeposition (#3762)Gravatar Andrew Myers 4-3/+46
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2023-03-27Docs: start using BibTeX in theory section (#3787)Gravatar Edoardo Zoni 4-376/+400
* Docs: start using BibTeX in theory section
2023-03-27AMReX: Weekly Update (#3788)Gravatar Axel Huebl 5-5/+5
2023-03-26CI: macOS allow deprecated declarationsGravatar Axel Huebl 1-1/+1
Will be updated via #3771
2023-03-25Update `updateAMReX.py` to match new CUDA yml file (#3772)Gravatar Edoardo Zoni 1-2/+2
* Update `updateAMReX.py` to match new CUDA yml file * Literal `.` in Regex Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2023-03-25ParaView: Add More Docs (#3785)Gravatar Axel Huebl 1-3/+30
* ParaView: Add More Docs Add hints, known issues and work-arounds.
2023-03-24include std::set, int template parameter (#3786)Gravatar Ryan Sandberg 1-1/+2
2023-03-24Refactoring of main.cpp to improve readability (#3784)Gravatar Luca Fedeli 13-34/+208
* refactoring of main.cpp to improve readability * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fixed bug --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
2023-03-24Workaround for nvcc (#3782)Gravatar Weiqun Zhang 3-24/+24
Fixes an issue in #3696. CUDA device lambda appears to have a limitation that explicit by-copy captures in addition to by-copy capture default would result in invalid device function at runtime.
2023-03-24Add FieldEnergy diagnostic in RZ (#3779)Gravatar David Grote 2-5/+74
* Add FieldEnergy diagnostic in RZ * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update Source/Diagnostics/ReducedDiags/FieldEnergy.cpp Use `nodeCentered` directly. Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * Update Source/Diagnostics/ReducedDiags/FieldEnergy.cpp NODE is not needed Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * Bug fix from previous commit --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2023-03-23Fix "modernize-loop-convert" issues found with clang-tidy (#3774)Gravatar Luca Fedeli 8-58/+61
* Fix all the modernize-loop-convert issues found with clang-tidy * Fix bug * Implement @EZoni's suggestions
2023-03-23Gaussian beam: allow 8-fold symmetry option (#3768)Gravatar Ryan Sandberg 6-9/+57
* add 8-fold beam symmetrization * Improve docs and fix examples * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fix signature bug, can compile * fix example * Apply suggestions from code review Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com> --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
2023-03-23Fix typos and comments from #3708 (#3770)Gravatar Phil Miller 1-7/+8
2023-03-23Fix add_particles to account for theta attribute with RZ (#3776)Gravatar David Grote 2-4/+17
* Fix add_particles to account for theta attribute with RZ * Add assertions in the number of attributes specified
2023-03-23PICMI Boundary: Silver-Mueller (#3709)Gravatar Axel Huebl 4-3/+4
* PICMI Boundary: Silver-Mueller Add support for silver-mueller boundary conditions in PICMI. * Dependencies: Update PICMI
2023-03-23fix modernize use equals default check by clang tidy (#3775)Gravatar Luca Fedeli 2-4/+8
2023-03-22CI: clean up Langmuir tests (#1613)Gravatar David Grote 13-82/+87
* Rewrote README for Langmuir regression tests * Removes the Python_Langmuir regression test * Update to include 1-D * Clean up file names --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Edoardo Zoni <ezoni@lbl.gov>
2023-03-21AMReX: Weekly Update (#3767)Gravatar Axel Huebl 4-4/+4
2023-03-20[mini] Print full json file if checksum CI fails (#3753)Gravatar Maxence Thévenet 2-1/+11
* print full json file if checksum CI fails. Make 1 test fail on purpose for illustration * Update Regression/Checksum/benchmarks_json/Deuterium_Deuterium_Fusion_3D.json
2023-03-20Crusher (OLCF): ADIOS 2.8.3 (#3759)Gravatar Axel Huebl 2-18/+1
New module for `adios2/2.8.3` received :tada:
2023-03-20PICMI: add `do_not_push` and `do_not_gather` (#3766)Gravatar Yinjian Zhao 1-0/+10
2023-03-17Add G in `CheckGuardCells` (needed w/ div(B) cleaning) (#3761)Gravatar Olga Shapoval 1-0/+10
2023-03-17Removed notes which were no longer restrictions on the allowed values of ↵Gravatar Grant Johnson 1-4/+0
amr.ref_ratio, amr.ref_ratio_vect (#3763)
2023-03-17Allow using different types for coordinates and values in {bi,tri}-linear ↵Gravatar Luca Fedeli 1-12/+19
interpolation functions (#3756) * change {bi,tri}-linear interpolation functions so that a different type can be used for coordinates and values * fixed bug
2023-03-16CI: fix bug in NVCC GNUMake yml file (#3765)Gravatar Edoardo Zoni 1-1/+1
2023-03-16Coulomb collisions: fix roundoff issues w/ gamma close to 1 (#3708)Gravatar David Grote 1-2/+5
2023-03-16Fix typo in docstring (#3755)Gravatar Luca Fedeli 1-1/+1
2023-03-16Fix typo in error message (#3760)Gravatar Olga Shapoval 1-1/+1
2023-03-14Sort `FieldProbe` output using probe particle ids (#3746)Gravatar Roelof Groenewald 2-22/+48
* Sort FieldProbe output using probe particle ids * increase noutputs by 1 rather than using +1 in several places * clean up comments * Improve inline comments Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2023-03-14remove spaces from headers in `FieldMaximum`, `RhoMaximum` and ↵Gravatar Arianna Formenti 3-15/+15
`ParticleNumber` red diags (#3751) * removed spaces from headers * removed spaces also from ParticleNumber red diag
2023-03-13NERSC: Update againGravatar Axel Huebl 1-0/+1
Missing newline
2023-03-13NERSC: Jupyter Kernel HelperGravatar Axel Huebl 1-0/+8
Make explicit what the NERSC docs skip.
2023-03-13Fix figure reference in docs for input+output (#3741)Gravatar Marco Garten 1-4/+3
2023-03-13Docs: fix default of `warpx.n_field_gather_buffer` (#3710)Gravatar Edoardo Zoni 1-12/+6
* Docs: fix default of `warpx.n_field_gather_buffer` * Add full syntax for default value
2023-03-13Deposition: Fix LB Cost Segfault (#3738)Gravatar Axel Huebl 2-3/+3
We sometimes call depositions before the load balance cost arrays are allocated, e.g., during initialization. In this case, we need to avoid writing into invalid memory.
2023-03-13AMReX: Weekly Update (#3750)Gravatar Axel Huebl 5-5/+5
2023-03-10PICMI: add missing flags for latest algorithms (#3743)Gravatar Edoardo Zoni 1-2/+76
* PICMI: add missing flags for latest algorithms * Fix docstrings
2023-03-10Fix Bucket __getattr__ (#3747)Gravatar David Grote 1-1/+1
2023-03-09Implement PICMI flag to set `compute_max_step_from_btd` (#3740)Gravatar Remi Lehe 1-0/+7
* Implement PICMI flag for setting max_step from btd * Update Python/pywarpx/picmi.py Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com> --------- Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
2023-03-09Spack: OpenMP w/o GPU (#3744)Gravatar Axel Huebl 2-6/+6
Spack desktop environments: Make sure that we are explicit about not matching GPU packages if we want to build a pure OpenMP version on a GPU-enabled machine.
2023-03-09New user input for grid type (collocated, staggered, hybrid) (#3683)Gravatar Edoardo Zoni 65-267/+339
* Introduce `warpx.grid_type` parameter * Replace `or` with `||` * Update examples with new user input syntax * Fix `if` condition * Improve error message * Fix `if` condition * Fix bugs * Fix warning * Fix RZ * Debugging * Fix RZ * Fix bug * Clean up * More changes: - set default algo parameters with hybrid grid - all hybrid input parameters under warpx name * Set default field gathering algo for hybrid grids * Update documentation
2023-03-08Fix typo in a comment (#3736)Gravatar Pierre-Bartoli 1-2/+2
Co-authored-by: Pierre Bartoli <pierre.bartoli@cea.fr>
2023-03-08Fix handling of name passed into SetTag (#3735)Gravatar David Grote 2-10/+10
* Fix handling of name passed into SetTag * Make name a reference in AddToMultiFabMap
2023-03-08Doc: Fix Builds, Disable all but HTML (#3737)Gravatar Axel Huebl 6-19/+21
PDF builds are brittle from auto-converted doc files we include in the theory sections. Disable PDF, fix other build errors for HTML.
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